Final Fantasy III's plot happened because the antagonist was stripped of his immortality as a reward for mastering magic. The entire game could've been avoided if the "villain"'s master thought for a moment about what he was doing before making him mortal, or allowed him to trade rewards with one of his two fellow students, who consider mortality to be a gift.
The Crowning Moment of Stupidity comes when one of your party members blows himself up for absolutely no reason whatsoever.
The above example only hints with what's really wrong with FF4: the game's tendency to make too many of its heroes commit acts of self-sacrifice, simply to shuffle new characters into the mix. With Tellah (who died trying to summon meteor to kill Golbez) and The Black/White Mage twins (who turned into stone to stop moving walls from crushing the heroes), those acts made sense. But when later characters do the same thing with increasingly arbitrary methods, players have a very hard time suspending disbelief. Exactly how does a monk with no experience with technology manage to stop an exploding computer, or how does a mechanic bombing the entrance to a world seal it away? To make the entire thing even dumber, with the exception of Tellah, all of the dead heroes came back, having survived their near-death experiences.
Worse still after having defeated the main antagonist in battle right before he can steal one of the last MacGuffins, they just turn around and walk out leaving him on the floor where he promptly gets up, takes the MacGuffin and warps away. Seriously. Particularly baffling considering the fact that it's a plot point that the main antagonist is out trying to get one of the MacGuffins when they assault his tower. They easily could have just repelled him the first time only for him to come back and steal it when they were busy storming his tower. Would certainly make a lot more sense then just ignoring him after his defeat.
In Final Fantasy V, at one point Exdeath tricks the party into destroying the spirits guarding the Crystals in Galuf's world. The party fell for this despite the fact that this involved a boss fight with exactly four enemies, each visibly crystalline in form, and each using spells of a specific element, and they had seen Exdeath trick others into destroying Crystals on at least three separate occasions already.
This in a game that started with the (unexpected and devastating) destruction of the Wind Crystal, after which no one in authority showed any interest in listening to you about the danger to the Water or Fire crystals.
Dirge of Cerberus hits this hard. The end of the world crisis this time is brought about by an underground sector who intends to wake up Omega Weapon by causing a relatively small scale genocide, which is supposed to prompt Omega Weapon to wake up and take the life force to another planet. Mind you, Meteor wasn't enough to wake up Omega and to be fair to the developers, Omega Weapon wasn't a thing at all in FFVII, but here the monster is going to make its decision to wipe out the planet's life after a very small-scale genocide. Compared to Meteor that was going to destroy everything. The Dark Id said it best as Cid.
Reeve:(normal game dialogue) Normally, Omega poses no threat to us. It only manifests when the planet has detected something that may cause her danger. ... By slaughtering thousands of innocent souls, they are creating a pure Lifestream in order to trick the planet into thinking the "end" is near. Cid:(The Dark Id's dialogue) Wait. Wait. Wait. Now wait just a fuckin' second here. Let me get this straight... We're going to all this trouble fighting these blowhards all because the planet is... fucking... RETARDED?!
The end of the first disc of Final Fantasy VIII is rife with people making bad decisions. Rinoa has her Odine Bangle plot, which depends entirely on a powerful sorceress not only being unaware of what it does, but willing to believe that a random girl got past security unannounced to give her a nice, totally trustworthy present. Then you have Quistis criticizing this plan, going all the way to her mission objective point, and then changing her mind and wanting to apologize right that minute instead of finishing the mission first, which wastes a huge amount of time and almost ruins everything. Then you have Irvine, who waits until the very last second to admit that he's actually a terrible sniper because he chokes under pressure and although this is probably a lie to get out of shooting Edea, he still only comes up with that lie right at the last second. Then, after Irvine finally decides to shoot Edea, she casually blocks the bullet with a Force Field, which makes someone wonder if the whole assassination plan could even have worked.
The Sanctum initiates the Purge to eliminate a handful of Pulse l'Cie, all of whom have visible brands on their bodies! The brands are common knowledge, and they sometimes even GLOW!
The only reason there even ARE Pulse l'cie on Cocoon is because the authorities on Cocoon used a big chunk of Pulse as building material without noticing the Pulse fal'cie that was inside. This happened hundreds of years ago.
And by the way, the highest authorities on Cocoon are fal'cie and l'cie, who would have personal experience with how these things work even if it weren't common knowledge.
The party can't seem to figure out whether their job is to save Cocoon, destroyCocoon, save Cocoonby destroying it, or something else entirely, nor can they agree on whether or not they're going to actually DO this job. And THAT's without them spending almost 10 of the 13 chapters trying to kill each other or abandon each other in the process. All they get is a cryptic vision of a giant monster (with no indication if they're supposed to stop it, kill it, help it, become it, or if it's some kind of threat about what will happen to them if they fail), some old legends, and the cryptic last words of a woman most of them didn't even know as she turned to crystal.
The above point bears a special mention to why this is all an idiot plot. The Fal'Cie give out a mission called a focus. This focus is a hazy image at best with no words or clues provided. Say for example, you get a hazy image of Barack Obama. You have no idea whether you're supposed to kill him, protect him, make him rock out to Slayer, throw a rock at him, ANYTHING, let alone where you're supposed to find him or meet him! The failure rate on this alone is absurdly high. And what makes this all stupid is that right near the end game, the Fal'Cie reveal that they can indeed talk and choose not to just tell people what their focus is. Now, give that kind of image to six people who have and want next to nothing to do with each other, and you have a plot based on contrivance and frankly, aggravation.
There are two characters in the very first chapter who know the answers to these questions, but one of them never speaks at all, and the other is keeping it a secret.
Eventually, Vanille comes to the conclusion that since the Big Bad's plan involves someone in their group, the best thing to do is to do nothing at all. Even after generally agreeing with her, they still charge on like nothing. Despite Cid telling them the exact same thing literally seconds later.
There's a few instances in Final Fantasy XIV, but the biggest crowner would have to be the backstory of the 6th Astral Era's War of the Magi, which would become the basis for the Scholar and Red Mage questlines and the Shadow's of Mhach raid series. During the War, the city of Mhach turned to forbidden void and summoning magics to draw in powerful demons from the void. Though the summoners took precautions, after summoning an extremely powerful voidsent named Diabolos, the top summoners started taking the Obviously Evil demon's advice at face value. Naturally, said advice was intentionally flawed and resulted in the 6th Calamity which resulted in Mhach being destroyed in a massive flood and their safe havens overrun with voidsent.